Open chromatin assays are known to have significant GC bias. Please take this
into consideration as necessary.
Library complexity quality metrics
Library complexity (filtered non-mito BAM)
rep1
rep2
ctl1
ctl2
Total Fragments
18898183
15087835
32995141
33667992
Distinct Fragments
16661928
12325157
31510018
33060330
Positions with Two Read
1728736
1920127
1371423
582759
NRF = Distinct/Total
0.881668
0.816894
0.95499
0.981951
PBC1 = OneRead/Distinct
0.882152
0.812897
0.954745
0.982062
PBC2 = OneRead/TwoRead
8.502373
5.217924
21.936371
55.71307
Mitochondrial reads are filtered out by default.
The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads
in a dataset; it is the ratio between the number of positions in the genome
that uniquely mapped reads map to and the total number of uniquely mappable
reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations
with EXACTLY one read pair over the genomic locations with AT LEAST one read
pair. PBC1 is the primary measure, and the PBC1 should be close to 1.
Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking,
0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is
the ratio of genomic locations with EXACTLY one read pair over the genomic
locations with EXACTLY two read pairs. The PBC2 should be significantly
greater than 1. See more details at
the ENCODE portal standard for ChIP-Seq pipeline
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'
Number of raw peaks
rep1
rep2
Number of peaks
299970
299961
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
136.0
116.0
134.0
134.0
25 percentile
544.0
464.0
390.0
536.0
50 percentile (median)
544.0
464.0
536.0
536.0
75 percentile
544.0
464.0
536.0
536.0
Max size
895.0
642.0
2048.0
2048.0
Mean
531.8769276927693
462.9228866419301
462.7303988133787
506.2361067710475
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures (trimmed/filtered SE BAM)
rep1
rep2
Number of Subsampled Reads
15000000
15000000
Estimated Fragment Length
220
145
Cross-correlation at Estimated Fragment Length
0.223043307010574
0.143842563586747
Phantom Peak
105
105
Cross-correlation at Phantom Peak
0.2035939
0.1430669
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.1390022
0.1250292
NSC (Normalized Strand Cross-correlation coeff.)
1.604603
1.150472
RSC (Relative Strand Cross-correlation coeff.)
1.301113
1.043003
Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50.
Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only.
Untrimmed FASTQs are used for all the other analyses.
NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.
Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value
rep1rep2
Jensen-Shannon distance (filtered/deduped BAM)
rep1
rep2
AUC
0.19589033533378858
0.2268277432831919
Synthetic AUC
0.4912863444815962
0.48988931529594604
X-intercept
0.2102407711074671
0.2314862216534016
Synthetic X-intercept
3.4246058163589143e-112
4.906028279462881e-83
Elbow Point
0.6785145782506099
0.5801923769147702
Synthetic Elbow Point
0.5107175094015904
0.49615660764024844
JS Distance
0.2645089783624122
0.14921820089347657
Synthetic JS Distance
0.38592318980169826
0.2966816490656603
% Genome Enriched
22.589889213294406
31.483421989361275
Diff. Enrichment
35.441344826725214
30.970241686696532
CHANCE Divergence
0.3051365120826033
0.2663707338397109
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for spp raw peaks
rep1
rep2
rep1-pr1
rep2-pr1
rep1-pr2
rep2-pr2
pooled
pooled-pr1
pooled-pr2
Fraction of Reads in Peaks
0.3182770565454629
0.212347536935532
0.3264890425734148
0.18029454226121286
0.3262569658876173
0.18082205930766312
0.25892851370874614
0.2680722433407498
0.2680834626084613
FRiP for overlap peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.16264739550641122
0.22737553939425315
0.08089274139467516
0.18228646295691253
FRiP for IDR peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.10840127897156808
0.1640139570567381
0.048549433690636266
0.1292620559726196
For spp raw peaks:
repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)
For overlap/IDR peaks:
repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates